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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Towards On-Chip Learning for Low Latency Reasoning with End-to-End Synthesis

The Software Defined Architectures (SODA) Synthesizer is an open-source compiler-based tool able to automatically generate domain-specialized systems targeting Application-Specific Integrated Circuits (ASICs) or Field Programmable Gate Arrays (FPGAs) starting from high-level programming. SODA is composed of a frontend, SODA-OPT, which leverages the multilevel intermediate representation (MLIR) framework to interface with productive programming tools (e.g., machine learning frame-works), identify kernels suitable for acceleration, and perform high-level optimizations, and of a state-of-the-art high-level synthesis backend, Bambu from the PandA framework, to generate custom accelerators. One specific application of the SODA Synthesizer is the generation of accelerators to enable ultra-low latency inference and control on autonomous systems for scientific discovery (e.g., electron microscopes, sensors in particle accelerators, etc.). This paper provides an overview of the flow in the context of the generation of accelerators for edge processing to be integrated in transmission electron microscopy (TEM) devices, focusing on use cases from precision material synthesis. We show the tool in action with an example of design space exploration for inference on reconfigurable devices with a conventional deep neural network model (LeNet). Finally, we discuss the research directions and opportunities enabled by SODA in the area of autonomous control for scientific experimental workflows.

Castellana, Vito G.↗
DOE OSTI2024

CMLM (Co-Optimized Machine-Learned Manifolds) [SWR-23-41]

Co-optimized Machine-Learned Manifolds (CMLM) is a data-driven approach for developing reduced-order manifold models for high-dimensional chemically reacting systems. It involves a specially designed neural network, the training of which simultaneously optimizes linear combinations of species that define the manifold, nonlinear mapping to outputs of interest such as reaction rates, and (optionally) subfilter closure for large eddy simulation. This software package provides an implementation of the CMLM approach in Python using the PyTorch machine learning library. A few example cases are included, showing how the tool can be applied to different types of data from 0D and 1D reacting simulations performed using Cantera. The neural networks can be saved in a format that is readable by the Pele suite of combustion solvers for use in reacting computational fluid dynamics simulations. This software repository contains several python scripts to perform various tasks associated with the Co-optimized Machine Learned Manifolds (CMLM) model, which is described in Perry, Henry de Frahan, and Yellapantula, CNF, 2022 (https://doi.org/10.1016/j.combustflame.2022.112286). This includes not only the code that defines the CMLM model, but also scripts to generate suitable training data, scripts to pre-process the data, scripts to train the CMLM model, and scripts to plot the output, as well as various other helper files. The scripts depend on several commonly used python libraries for data analysis and chemical reaction computations. The trained models that result from this tool are designed to work with the an interface being implemented in the Pele suite of reacting flow solvers (https://github.com/AMReX-Combustion).

Perry, Bruce↗
DOE OSTI2020

Beowulf v2.5.3 User Guide: Revision 5

This document is a user guide for the Beowulf (rebranding of Watchmen) tool. It describes how operators can access and utilize the application's functionality. Beowulf is a research software application developed by Pacific Northwest National Laboratory (PNNL) that incorporates the scientific and operational expertise for reviewing data from treaty monitoring radionuclide stations. These stations are part of a worldwide network to monitor for nuclear explosions, and the data they produce are critical to make the determination of whether a sample is from a nuclear explosion or some other source (i.e., nuclear reactor or medical isotope production facility). Stations deliver their measurements and system status to the International Monitoring System (IMS), which forwards it via email to all subscribers. Beowulf is capable of processing data from several radioxenon station types and development is in progress on a solution for particulate stations. Screening of data in Beowulf may be done by a number of different users such as radionuclide analysts, evaluators, and data quality experts. This guide is provided to assist those users in navigating the application. The term Beowulf is used generically throughout this document to refer to any of the various components in the software application. The user interface that is viewed with a web browser is the primary focus of this user guide. Other components include a database to store measurements and state of health (SOH) data; and the data loader that monitors incoming emails, parses the data, populates the database, does the initial analysis, and routes data for review.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

WHONDRS-GUI: a web application for global survey of surface water metabolites

Background The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. Results The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811 , which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server ( https://xmlin.shinyapps.io/whondrs/ ).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Hydrogen bonding structure of confined water templated by a metal-organic framework with open metal sites

Abstract Water in confinement exhibits properties significantly different from bulk water due to frustration in the hydrogen-bond network induced by interactions with the substrate. Here, we combine infrared spectroscopy and many-body molecular dynamics simulations to probe the structure and dynamics of confined water as a function of relative humidity within a metal-organic framework containing cylindrical pores lined with ordered cobalt open coordination sites. Building upon the agreement between experimental and theoretical spectra, we demonstrate that water at low relative humidity binds initially to open metal sites and subsequently forms disconnected one-dimensional chains of hydrogen-bonded water molecules bridging between cobalt atoms. With increasing relative humidity, these water chains nucleate pore filling, and water molecules occupy the entire pore interior before the relative humidity reaches 30%. Systematic analysis of rotational and translational dynamics indicates heterogeneity in this pore-confined water, with water molecules displaying variable mobility as a function of distance from the interface.

Science & Technology - Other Topics↗
DOE OSTI2022

LungMAP Portal Ecosystem: Systems-level Exploration of the Lung

An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular, imaging, and pathological datasets. To centralize and standardize information across broad lung research efforts we expanded the LungMAP.net website into a new gateway portal. This portal connects a broad spectrum of research networks, bulk and single-cell multi-omics data and a diverse collection of image data that span mammalian lung development, and disease. The data are standardized across species and technologies using harmonized data and metadata models that leverage recent advances including those from the Human Cell Atlas, diverse ontologies, and the LungMAP CellCards initiative. To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, mouse), to enable consistent queries across technologies, cohorts, age, disease, and drug treatment. These atlases are provided as independent and integrated queryable datasets, with an emphasis on dynamic visualization, figure generation, re-analysis, cell-type curation, and automated reference-based classification of user-provided single-cell genomics datasets (Azimuth). Finally, as this resource grows, we intend to increase the breadth of available interactive interfaces, supported data types, data portals and datasets from LungMAP and external research efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q1

Microbes play key roles in our biosphere, from driving global nutrient cycling to impacting plant, animal and human health and disease. Complex data from microbial genomes, proteins, and metabolites provide a window into these tiny engines that drive life on our planet. Yet these data are dispersed among researchers’ laboratories and various repositories, making it difficult to access. This calls for new ways of managing data, improving data interoperability, advancing community standards, and creating an infrastructure where data are shared efficiently. We have built the National Microbiome Data Collaborative (NMDC) to advance how scientists create, use, and reuse data to redefine the way we understand and harness the power of microbes. The vision of the National Microbiome Data Collaborative (NMDC) is to drive a microbiome data sharing network connecting data, people, and ideas to advance microbiome innovation and discovery. The NMDC was launched in 2019 and brought together DOE National Laboratories to collaborate across resources, capabilities, and expertise. The NMDC team was strategically assembled to include software developers, microbial researchers, metadata experts, and multi-omics specialists. The diversity of the NMDC team reflects the inherently interdisciplinary nature of microbiome science, and we leverage the strengths of the DOE National Laboratory system. Towards BER’s goal of advancing an iterative systems biology approach to the understanding of microbial genomes, the NMDC serves as a foundation for infrastructure, data standards, and community building. Together with the flagship DOE User Facilities, the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), we are developing core capabilities in metadata standards for environmental descriptors and sample handling and processing; standardized bioinformatic workflows; an interface for data search and access; and robust community engagement activities. The NMDC production platform supports long-term data infrastructure and community building for BER’s bioenergy and environmental research goals. Our approach leverages lessons learned and an ambitious framework for collaborative, interdisciplinary data infrastructure to support microbiome research. The NMDC supports data, information, and knowledge access through three defined software tools – the Submission Portal, NMDC EDGE, and the Data Portal – driven by community needs. Herein, we describe the value proposition for the microbiome research community, our overarching strategy, and challenges and opportunities for developing the NMDC as both an infrastructure and community engagement program.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

LEED: A Lightwave Energy-Efficient Datacenter

The Lightwave Energy-Efficient Datacenter (LEED) program is a disruptive “green-field” approach that provides a quantum leap in the energy efficiency of datacenters. LEED’s fundamental value proposition is that a novel and re-architected optical network—RotorNet— can deliver “more bandwidth per buck” as well as unique system-level attributes that significantly improve overall datacenter energy efficiency and performance. LEED has developed three system-level testbeds. The first testbed uses calibrated hardware and software power measurements to determine server energy efficiency as a function of network bandwidth and workload. These measurements have shown that increasing network communications bandwidth dramatically increases server energy efficiency providing a realistic path to the overall ENLITENED program goal of doubling the number of transactions per joule. The second testbed demonstrates key hardware: a prototype low-loss, high-port count optical “selector switch”. This switch was fabricated, racked, and tested. Measured switch characteristics include loss, bandwidth, crosstalk, switch time, system-level switch time (including the transceivers), and bit error rate. The third testbed demonstrates a fully working and manufactured pinwheel design which dramatically lowers the cost of design, while delivering high switch radix and low reconfiguration times. The LEED project has tied these three novel photonic switch prototypes together with production servers and software through the development of a novel FPGA-based NIC platform called Corundum. Corundum ensures that the packet-switched protocols supported by commodity operating systems and devices can interface with the Rotor switch design. The LEED group has used this combined hardware and software prototype to characterize applications running at a commercially relevant scale. The project has used a combination of enhanced optical modulation amplitude (OMA) modulators, broadband multiplexers and demultiplexers, avalanche photodiodes, and a novel burst-mode receivers to enable the insertion of LEED-developed optical switches without the need for expensive optical amplification. Our modeling has shown that measured LEED-developed device characteristics can achieve link characteristics of 2 pJ/bit including both transceivers and the Rotor switch. In summary, the LEED program has demonstrated a credible and practical path, through novel hardware and software, to realize the program objectives of ENLITENED. The net result will ensure that the United States maintains its strength in the crucial sector of Information Technology, which is vital to both our economic security and our national security.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

VRN3P: Variational Recurrent Neural Network Based Net-Load Prediction under High Solar Penetration

This is the final technical report for the SETO-funded VRN3P project (PNNL# 76914). The goal of this project, led by Pacific Northwest National Laboratory (PNNL), in collaboration with Lawrence Livermore National Laboratory (LLNL) and Portland General Electric (PGE), was to develop and validate a deep variational recurrent neural network-based net-load prediction (VRN3P) framework for probabilistic time-series forecasting of day-ahead net-load under high solar penetration scenarios. The project team reports successful design of a novel probabilistic net-load forecasting architecture, comprising of a variational autoencoder and a recurrent neural network, which demonstrates 30% improvement in forecast performance, 60% improvement in training time, and consumes 44% less memory, when compared with conventional baseline models. The team tested the VRN3P model performance on GridLAB-D test-cases representing varying BTM solar penetration levels of 20%, 30%, and 50%, with integrated time-series net-load profiles provided by the utility partner (PGE). The VRN3P model demonstrate <2% hourly MAPE (averaged over the year) for day- ahead net-load forecast on the test scenario with 20% BTM solar. Transfer learning extension of the VRN3P model has demonstrated 8.33× speed-up in training, while still achieving acceptable forecast performance of 2.24% hourly MAPE on the 30% BTM solar penetration test-scenario. A preliminary version of the VRN3P GridAPPS-D™has been developed, along with a web-based interactive user-interface (named ‘Forte’) which has made available on GitHub for public use.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Insights on seasonal solifluction processes in warm permafrost Arctic landscape using a dense monitoring approach across adjacent hillslopes

Solifluction processes in the Arctic are highly complex, introducing uncertainties in estimating current and future soil carbon storage and fluxes, and assessment of hillslope and infrastructure stability. This study aims to enhance our understanding of triggers and drivers of soil movement of permafrost-affected hillslopes in the Arctic. To achieve this, we established an extensive soil deformation and temperature sensor network, covering 48 locations across multiple hillslopes within a 1 km² watershed on the Seward Peninsula, AK. We report depth-resolved measurements down to 1.8 m depth for May to September 2022, a period conducive to soil movement due to deepening thaw layers and frequent rain events. Over this period, surface movements of up to 334 mm were recorded. In general, these movements occur close to the thawing front, and are initiated as thawing reaches depths of 0.4 to 0.75 m. The largest movements were observed at the top of the south-east facing slope, where soil temperatures are cold (mean annual soil temperatures averaging -1.13°C) and slopes are steeper than 15°. Our analysis highlights three primary factors influencing movements: slope angle, soil thermal conditions, and thaw depth. The latter two significantly impact the generation of pore water pressures at the thaw–freeze interface. Specifically, soil thermal conditions govern the liquid water content, while thaw depth influences both the height of the water column and, consequently, the pressure at the thawing front. These factors affect soil properties, such as cohesion and internal friction angle, which are crucial determinants of slope stability. This underscores the significance of a precise understanding of subsurface thermal conditions, including spatial and temporal variability in soil temperature and thaw depth, when assessing and predicting slope instabilities. Based on our observations, we developed a Factor of Safety proxy that consistently falls below the triggering threshold for all probes exhibiting displacements exceeding 50 mm. This study offers novel insights into patterns and triggers of hillslope movements in the Arctic and provides a venue to evaluate their impact on soil redistribution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Cluster expansion by transfer learning for phase stability predictions

Recent progress towards universal machine-learned interatomic potentials holds considerable promise for materials discovery. Yet the accuracy of these potentials for predicting phase stability may still be limited. In contrast, cluster expansions provide accurate phase stability predictions but are computationally demanding to parameterize from first principles, especially for structures of low dimension or with a large number of components, such as interfaces or multimetal catalysts. We overcome this trade-off via transfer learning. Using Bayesian inference, we incorporate prior statistical knowledge from machine-learned and physics-based potentials, enabling us to sample the most informative configurations and to efficiently fit first-principles cluster expansions. Furthermore, this algorithm is tested on Pt:Ni, showing robust convergence of the mixing energies as a function of sample size with reduced statistical fluctuations.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Microstructure and creep properties of cast near-eutectic Al–Ce–Ni alloys

This study investigates the as-cast and aged microstructures, thermal stability, ambient temperature strengthening, and creep resistance of three ternary Al–Ce–Ni alloys (wt%): near-eutectic Al–10Ce–5Ni (with both eutectic and hypoeutectic regions), hypoeutectic Al-7.5Ce-3.75Ni (with numerous primary Al dendrites), and hypereutectic Al-12.5Ce-6.25Ni (with coarse, blocky primary Al3Ni and Al11Ce3 precipitates and some primary Al dendrites). Depending on the alloy composition and local solidification conditions, the following eutectic morphologies are found: (i) coarse Al–Ce eutectic colonies where Al 11 Ce 3 is in the form of “Chinese script”, (ii) intermingled regions of binary Al–Ce and Al–Ni eutectic colonies, with finer Al 3 Ni and Al 11 Ce 3 fibers, (iii) large ternary eutectic colonies, where the binary Al 3 Ni and Al 11 Ce 3 phases are alternating or intertwining within the individual, fine fibers (diameters of ~60–170 nm, depending on solidification rates), and (iv) ternary eutectic zones (between primary Al dendrites), where fine Al 3 Ni and Al 11 Ce 3 build up a 3D-interconnected network. The high volume fraction of intermetallic phases and extremely fine eutectic spacing/fiber diameter both contribute to high ambient strengthening (higher as-cast microhardness than binary Al–Ce or Al–Ni), and also provide enhanced creep resistance at 300 and 350 °C. Additionally, the alloys are coarsening-resistant up to 425 °C for extended periods, with a gradual decrease in microhardness. The alloys aged at 400 °C to 1050 h show fiber fragmentation and coarsening of the resulting particles, with the faster-diffusing Ni driving more rapid coarsening of the Al 3 Ni particles which engulf finer, more stable Al 11 Ce 3 particles. Severe overaging (performed at 590 °C for 24 h) leads to Al 3 Ni and Al 11 Ce 3 spheroids which remain submicron-sized in eutectic colonies, but micron-sized at colony boundary and at Al dendrite-eutectic interface. Creep resistance at 300 °C of overaged Al–10Ce–5Ni remains substantial, consistent with load-transfer based composite strengthening being an important strengthening mechanism in these alloys, making them excellent candidates for replacement of heavier steel or titanium parts operating under stress up to 300 °C.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Interfacial Hydrogen-Bond Dynamics in Transition Metal Compounds

Understanding how water behaves when confined within atomic layers of active transition-metal carbides, nitrides, and carbonitrides is essential for uncovering the fundamental principles needed to engineer solid–liquid interfaces at the atomic scale. Yet, how lattice element chemistry and surface termination groups collectively regulate the structure and mobility of such interlayer water remains poorly understood. Here, we present a composition-controlled investigation of interlayer water dynamics in layered transition-metal nitride, carbide, and carbonitride systems using a systematic integration of quasi-elastic neutron scattering (QENS), ab initio molecular dynamics (AIMD) simulations, and density functional theory (DFT) calculations. QENS measurements show that nitride-rich systems host mobile, translationally diffusing water with thermally activated self-diffusion coefficients on the order of 10 –10 m 2 s –1 , whereas mixed C/N lattices confine water to localized, nontranslational motion that is insensitive to temperature. AIMD and DFT reveal that lattice C/N chemistry and surface functional group composition reshape the first hydration layer by modulating the surface electronic structure and termination-dependent hydrogen-bond networks, leading to pronounced differences in water ordering and thermal resilience. On the other hand, fully carbide systems exhibit intermediate behavior, highlighting that water mobility is not primarily controlled by the hydration level alone but by the coupling between lattice composition and surface chemistry. Overall, this study establishes how surface chemistry and lattice composition jointly control interfacial hydrogen bond dynamics, offering a mechanistic framework for designing transition-metal layered materials with tailored interfacial transport properties.

Hydration↗
DOE OSTI2022

Applications of Machine Learning to Predicting Core-collapse Supernova Explosion Outcomes

Most existing criteria derived from progenitor properties of core-collapse supernovae are not very accurate in predicting explosion outcomes. We present a novel look at identifying the explosion outcome of core-collapse supernovae using a machine-learning approach. Informed by a sample of 100 2D axisymmetric supernova simulations evolved with F ornax , we train and evaluate a random forest classifier as an explosion predictor. Furthermore, we examine physics-based feature sets including the compactness parameter, the Ertl condition, and a newly developed set that characterizes the silicon/oxygen interface. With over 1500 supernovae progenitors from 9-27 M ⊙ , we additionally train an autoencoder to extract physics-agnostic features directly from the progenitor density profiles. We find that the density profiles alone contain meaningful information regarding their explodability. Both the silicon/oxygen and autoencoder features predict the explosion outcome with ≈90% accuracy. In anticipation of much larger multidimensional simulation sets, we identify future directions in which machine-learning applications will be useful beyond the explosion outcome prediction.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Kinetically versus thermodynamically controlled factors governing elementary pathways of GaP(111) surface oxidation

GaP and related III-V semiconductors have attracted interest as high-efficiency photoelectrochemical electrodes for solar water splitting. However, their efficacy is linked to the presence, identity, and integrity of native surface oxides, which are structurally and chemically complex and evolve during operation. Using ambient pressure X-ray photoelectron spectroscopy (APXPS) coupled with ab initio simulations, we track key chemical motifs expressed during evolution of GaP(111) surface oxides, their associated reaction kinetics, and their correlations with electronic properties. We identify two distinct thermal regimes corresponding to kinetically and thermodynamically controlled oxidation. Below 600 K, exposure to O2 generates kinetically facile Ga-O-Ga configurations, whereas higher temperatures cause activated oxygen to insert into Ga–P bonds as part of a thermodynamically driven transformation into a complex, heterogeneous 3D network of surface POx (1≤x ≤ 4) groups and Ga2O3 species, the latter of which eventually dominates upon depletion of surface phosphorus. Here our study highlights the critical competition between kinetic and thermodynamic factors during GaP oxidation, yielding insights for fabricating stable III-P-based photoelectrodes with precisely engineered surface properties.

08 HYDROGEN↗
DOE OSTI2021

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

First measurement of the cross section for top quark pair production with additional charm jets using dileptonic final states in pp collisions at $\sqrt{s}$= 13 TeV

The first measurement of the inclusive cross section for top quark pairs ($t\bar{t}$) produced in association with two additional charm jets is presented. The analysis uses the dileptonic final states of $t\bar{t}$ events produced in proton-proton collisions at a centre-of-mass energy of 13 TeV. The data correspond to an integrated luminosity of 41.5 fb -1 recorded by the CMS experiment at the LHC. A new charm jet identification algorithm provides input to a neural network that is trained to distinguish among $t\bar{t}$ events with two additional charm ($t\bar{t}c\bar{c}$), bottom ($t\bar{t}b\bar{b}$), and light-flavour or gluon ($t\bar{t}LL$) jets. By means of a template fitting procedure, the inclusive $t\bar{t}c\bar{c}$, $t\bar{t}b\bar{b}$, and $t\bar{t}LL$ cross sections are simultaneously measured, together with their ratios to the inclusive $t\bar{t}$ + two jets cross section. This provides measurements of the $t\bar{t}c\bar{c}$ and $t\bar{t}b\bar{b}$ cross sections of 10.1 ± 1.2 (stat) ± 1.4 (syst) pb and 4.54 ± 0.35 (stat) ± 0.56 (syst) pb, respectively, in the full phase space. The results are compared and found to be consistent with predictions from two different matrix element generators with next-to-leading order accuracy in quantum chromodynamics, interfaced with a parton shower simulation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex

The alkane monooxygenase AlkB and rubredoxin AlkG form an electron transfer complex that hydroxylates terminal alkanes to produce alcohols. The recent cryoEM study of Fontimonas thermophila AlkB-AlkG complex revealed its architecture, including a dodecane (D12) substrate at the active site. However, FtAlkBG molecular mechanism of action of remains unknown. Here, in this study, we examined its dynamics and interactions by multiscale computations, including molecular dynamics simulations, elastic network models, and QM/MM of the oxygen activation mechanism at the AlkB catalytic site. D12 maintained stable interactions within the catalytic site during two MD runs, coordinated by hydrophobic residues L263-L264, I267, I133. A third extended run revealed that D12 could translocate to a membrane-exposed site near S49/F46 along a hydrophobic channel gated by I54. During this translocation, D12 was temporarily stabilized at intermediate sites IS1 (lined by I27/L30-G31/G50/L53-I54/P59/S124/A127-V128) and IS2 (I33-G34/L37/L45-F46/S49) before nearly exiting the protein, and diffused back to the active site, assisted by L30. Substrate binding and translocation across those intermediate sites affects the coupling between the iron centers in AlkBG, and interfacial interactions between AlkB-AlkG. The channel was further connected to the cytosol, near two surface-exposed arginines, potentially allowing for O 2 passage. The allosteric effects between D12 putative entry site, catalytic site and AlkB-AlkG interface were analyzed by ENM-based methods which confirmed the cooperative perturbation-responses and strongly correlated movements of residues belonging to those distal regions. Our study provides new mechanistic insights into key sites and their interactions that could be targeted for developing AlkB-variants with desirable alkane conversion functions.

59 BASIC BIOLOGICAL SCIENCES↗